| Chain sequence(s) |
C: QVQLKQSGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQSPGKGLEWLGMIWGDGRTDYKSALKSRLSITKDNSKSQVFLKMNSLQTDDTARYFCASDYYGSGSFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLESDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC
B: DVVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKSGQSPKLLIHSASYRYTGVPDRFTGSGSGTDFTFTISSVQAEDLAVYYCQQHYSIPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC input PDB |
| Selected Chain(s) | B,C |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:44)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/d2baedbcea4780f/tmp/folded.pdb (00:03:44)
[INFO] Main: Simulation completed successfully. (00:06:03)
|
The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan4D score | mutation |
|---|---|---|---|---|
| 1 | D | B | -1.3404 | |
| 2 | V | B | -0.1648 | |
| 3 | V | B | 0.9513 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -0.3794 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.2086 | |
| 8 | H | B | -1.6920 | |
| 9 | K | B | -1.8857 | |
| 10 | F | B | -0.5491 | |
| 11 | M | B | -0.3207 | |
| 12 | S | B | -0.3411 | |
| 13 | T | B | 0.0000 | |
| 14 | S | B | -0.6406 | |
| 15 | V | B | 0.3290 | |
| 16 | G | B | -1.0081 | |
| 17 | D | B | -2.3730 | |
| 18 | R | B | -2.6724 | |
| 19 | V | B | 0.0000 | |
| 20 | S | B | -0.4984 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8591 | |
| 23 | C | B | 0.0000 | |
| 24 | K | B | -1.9470 | |
| 25 | A | B | 0.0000 | |
| 26 | S | B | -1.1946 | |
| 27 | Q | B | -2.3353 | |
| 28 | D | B | -2.6226 | |
| 29 | V | B | 0.0000 | |
| 30 | S | B | -0.8112 | |
| 31 | T | B | -0.3541 | |
| 32 | A | B | 0.0243 | |
| 33 | V | B | 0.0000 | |
| 34 | A | B | 0.0000 | |
| 35 | W | B | 0.0000 | |
| 36 | Y | B | 0.0000 | |
| 37 | Q | B | 0.0000 | |
| 38 | Q | B | 0.0000 | |
| 39 | K | B | -1.5271 | |
| 40 | S | B | -1.3474 | |
| 41 | G | B | -1.4845 | |
| 42 | Q | B | -2.1578 | |
| 43 | S | B | -1.5191 | |
| 44 | P | B | 0.0000 | |
| 45 | K | B | -1.5469 | |
| 46 | L | B | 0.0000 | |
| 47 | L | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | H | B | 0.0000 | |
| 50 | S | B | 0.2185 | |
| 51 | A | B | 0.0000 | |
| 52 | S | B | 0.1413 | |
| 53 | Y | B | 0.9318 | |
| 54 | R | B | -0.2803 | |
| 55 | Y | B | 0.0241 | |
| 56 | T | B | -0.1164 | |
| 57 | G | B | -0.6861 | |
| 58 | V | B | -0.6671 | |
| 59 | P | B | -1.1693 | |
| 60 | D | B | -2.1345 | |
| 61 | R | B | -1.5881 | |
| 62 | F | B | 0.0000 | |
| 63 | T | B | -0.4747 | |
| 64 | G | B | 0.0000 | |
| 65 | S | B | -0.4800 | |
| 66 | G | B | -1.0519 | |
| 67 | S | B | -1.1000 | |
| 68 | G | B | -1.7324 | |
| 69 | T | B | -2.1946 | |
| 70 | D | B | -2.4166 | |
| 71 | F | B | 0.0000 | |
| 72 | T | B | -0.6959 | |
| 73 | F | B | 0.0000 | |
| 74 | T | B | -0.5713 | |
| 75 | I | B | 0.0000 | |
| 76 | S | B | -1.8044 | |
| 77 | S | B | -1.6226 | |
| 78 | V | B | 0.0000 | |
| 79 | Q | B | -0.6063 | |
| 80 | A | B | -0.3366 | |
| 81 | E | B | -1.2953 | |
| 82 | D | B | 0.0000 | |
| 83 | L | B | -0.0366 | |
| 84 | A | B | 0.0000 | |
| 85 | V | B | -0.1651 | |
| 86 | Y | B | 0.0000 | |
| 87 | Y | B | 0.0000 | |
| 88 | C | B | 0.0000 | |
| 89 | Q | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | H | B | 0.6302 | |
| 92 | Y | B | 1.1553 | |
| 93 | S | B | 0.7448 | |
| 94 | I | B | 0.8179 | |
| 95 | P | B | 0.1686 | |
| 96 | L | B | 0.0000 | |
| 97 | T | B | 0.3635 | |
| 98 | F | B | 0.3941 | |
| 99 | G | B | 0.0000 | |
| 100 | A | B | -0.6181 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | K | B | -0.5449 | |
| 104 | L | B | 0.0000 | |
| 105 | E | B | 0.0000 | |
| 106 | L | B | -0.4411 | |
| 107 | K | B | -1.8781 | |
| 108 | R | B | -1.9278 | |
| 109 | A | B | -1.5458 | |
| 110 | D | B | -2.5044 | |
| 111 | A | B | -1.3441 | |
| 112 | A | B | -0.6722 | |
| 113 | P | B | 0.0000 | |
| 114 | T | B | -0.1124 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | 0.0470 | |
| 117 | I | B | 0.0415 | |
| 118 | F | B | 0.0000 | |
| 119 | P | B | -0.2162 | |
| 120 | P | B | 0.0000 | |
| 121 | S | B | 0.0000 | |
| 122 | S | B | -0.7907 | |
| 123 | E | B | -1.2309 | |
| 124 | Q | B | 0.0000 | |
| 125 | L | B | -0.9993 | |
| 126 | T | B | -0.7296 | |
| 127 | S | B | -0.7731 | |
| 128 | G | B | -1.1996 | |
| 129 | G | B | -1.0824 | |
| 130 | A | B | 0.0000 | |
| 131 | S | B | 0.0000 | |
| 132 | V | B | 0.0000 | |
| 133 | V | B | 0.0000 | |
| 134 | C | B | 0.0000 | |
| 135 | F | B | 0.0000 | |
| 136 | L | B | 0.0000 | |
| 137 | N | B | 0.0000 | |
| 138 | N | B | -0.8176 | |
| 139 | F | B | 0.0000 | |
| 140 | Y | B | 0.0000 | |
| 141 | P | B | -2.0923 | |
| 142 | K | B | -2.0700 | |
| 143 | D | B | -2.5660 | |
| 144 | I | B | -1.6434 | |
| 145 | N | B | -1.5207 | |
| 146 | V | B | -0.5586 | |
| 147 | K | B | -1.2803 | |
| 148 | W | B | 0.0000 | |
| 149 | K | B | -2.1581 | |
| 150 | I | B | 0.0000 | |
| 151 | D | B | -2.3222 | |
| 152 | G | B | -1.7590 | |
| 153 | S | B | -2.0043 | |
| 154 | E | B | -3.0986 | |
| 155 | R | B | -2.7412 | |
| 156 | Q | B | -2.5175 | |
| 157 | N | B | -2.1298 | |
| 158 | G | B | -0.9407 | |
| 159 | V | B | -0.5079 | |
| 160 | L | B | 0.1734 | |
| 161 | N | B | -0.0355 | |
| 162 | S | B | 0.0000 | |
| 163 | W | B | 0.2560 | |
| 164 | T | B | -0.8141 | |
| 165 | D | B | -2.0492 | |
| 166 | Q | B | -1.8123 | |
| 167 | D | B | -2.2000 | |
| 168 | S | B | -1.8116 | |
| 169 | K | B | -2.3227 | |
| 170 | D | B | -1.7706 | |
| 171 | S | B | 0.0000 | |
| 172 | T | B | 0.0000 | |
| 173 | Y | B | 0.0000 | |
| 174 | S | B | 0.0000 | |
| 175 | M | B | 0.0000 | |
| 176 | S | B | 0.0000 | |
| 177 | S | B | 0.0000 | |
| 178 | T | B | 0.0976 | |
| 179 | L | B | 0.0000 | |
| 180 | T | B | -0.2441 | |
| 181 | L | B | 0.0000 | |
| 182 | T | B | -1.8162 | |
| 183 | K | B | -2.6013 | |
| 184 | D | B | -3.6227 | |
| 185 | E | B | -3.3955 | |
| 186 | Y | B | 0.0000 | |
| 187 | E | B | -3.5785 | |
| 188 | R | B | -3.8027 | |
| 189 | H | B | -2.9262 | |
| 190 | N | B | -2.4939 | |
| 191 | S | B | -1.7127 | |
| 192 | Y | B | 0.0000 | |
| 193 | T | B | -0.9490 | |
| 194 | C | B | 0.0000 | |
| 195 | E | B | -0.3806 | |
| 196 | A | B | 0.0000 | |
| 197 | T | B | -0.8091 | |
| 198 | H | B | 0.0000 | |
| 199 | K | B | -2.4078 | |
| 200 | T | B | -1.3832 | |
| 201 | S | B | -0.7632 | |
| 202 | T | B | -0.6002 | |
| 203 | S | B | -0.3209 | |
| 204 | P | B | -0.2193 | |
| 205 | I | B | 0.5898 | |
| 206 | V | B | 0.7545 | |
| 207 | K | B | -0.2048 | |
| 208 | S | B | -0.4336 | |
| 209 | F | B | 0.0000 | |
| 210 | N | B | -1.9176 | |
| 211 | R | B | -1.9924 | |
| 212 | N | B | -2.0439 | |
| 213 | E | B | -1.5983 | |
| 214 | C | B | -0.5011 | |
| 1 | Q | C | -1.4572 | |
| 2 | V | C | -0.8823 | |
| 3 | Q | C | -1.8288 | |
| 4 | L | C | 0.0000 | |
| 5 | K | C | -2.3664 | |
| 6 | Q | C | 0.0000 | |
| 7 | S | C | -0.8753 | |
| 8 | G | C | -0.3592 | |
| 9 | P | C | -0.2054 | |
| 10 | G | C | -0.1961 | |
| 11 | L | C | 0.5023 | |
| 12 | V | C | 0.0000 | |
| 13 | A | C | -0.4109 | |
| 14 | P | C | -0.9541 | |
| 15 | S | C | -1.3189 | |
| 16 | Q | C | -1.5732 | |
| 17 | S | C | -1.5659 | |
| 18 | L | C | 0.0000 | |
| 19 | S | C | -0.8812 | |
| 20 | I | C | 0.0000 | |
| 21 | T | C | -0.6439 | |
| 22 | C | C | 0.0000 | |
| 23 | T | C | -1.2603 | |
| 24 | V | C | 0.0000 | |
| 25 | S | C | -1.3418 | |
| 26 | G | C | -1.0197 | |
| 27 | F | C | -0.2006 | |
| 28 | S | C | -0.5170 | |
| 29 | L | C | 0.0000 | |
| 30 | T | C | -0.7709 | |
| 31 | G | C | -0.3123 | |
| 32 | Y | C | 0.7803 | |
| 33 | G | C | -0.1569 | |
| 34 | V | C | 0.0000 | |
| 35 | N | C | 0.0000 | |
| 36 | W | C | 0.0000 | |
| 37 | V | C | 0.0000 | |
| 38 | R | C | -0.8745 | |
| 39 | Q | C | 0.0000 | |
| 40 | S | C | -1.5157 | |
| 41 | P | C | -1.3670 | |
| 42 | G | C | -1.4424 | |
| 43 | K | C | -2.1245 | |
| 44 | G | C | -1.1553 | |
| 45 | L | C | 0.0000 | |
| 46 | E | C | -0.7879 | |
| 47 | W | C | 0.0000 | |
| 48 | L | C | 0.0000 | |
| 49 | G | C | 0.0000 | |
| 50 | M | C | -0.2063 | |
| 51 | I | C | 0.0000 | |
| 52 | W | C | -0.7978 | |
| 53 | G | C | -1.1268 | |
| 54 | D | C | -2.3095 | |
| 55 | G | C | -2.0446 | |
| 56 | R | C | -2.4618 | |
| 57 | T | C | -1.3038 | |
| 58 | D | C | -0.9162 | |
| 59 | Y | C | -0.7210 | |
| 60 | K | C | -1.0851 | |
| 61 | S | C | -1.2841 | |
| 62 | A | C | -0.7028 | |
| 63 | L | C | 0.0000 | |
| 64 | K | C | -2.1079 | |
| 65 | S | C | -1.3830 | |
| 66 | R | C | -1.5127 | |
| 67 | L | C | 0.0000 | |
| 68 | S | C | -1.1015 | |
| 69 | I | C | 0.0000 | |
| 70 | T | C | -0.8342 | |
| 71 | K | C | -1.2013 | |
| 72 | D | C | -1.8274 | |
| 73 | N | C | -2.3708 | |
| 74 | S | C | -1.9075 | |
| 75 | K | C | -2.5263 | |
| 76 | S | C | -1.7999 | |
| 77 | Q | C | -1.5612 | |
| 78 | V | C | 0.0000 | |
| 79 | F | C | -0.3283 | |
| 80 | L | C | 0.0000 | |
| 81 | K | C | -1.6124 | |
| 82 | M | C | 0.0000 | |
| 83 | N | C | -2.0121 | |
| 84 | S | C | -1.3777 | |
| 85 | L | C | 0.0000 | |
| 86 | Q | C | -2.1873 | |
| 87 | T | C | -1.5748 | |
| 88 | D | C | -2.2253 | |
| 89 | D | C | 0.0000 | |
| 90 | T | C | -0.9985 | |
| 91 | A | C | 0.0000 | |
| 92 | R | C | -1.1998 | |
| 93 | Y | C | 0.0000 | |
| 94 | F | C | 0.0000 | |
| 95 | C | C | 0.0000 | |
| 96 | A | C | 0.0000 | |
| 97 | S | C | 0.0000 | |
| 98 | D | C | 0.0607 | |
| 99 | Y | C | 0.5189 | |
| 100 | Y | C | 1.1901 | |
| 101 | G | C | 0.2102 | |
| 102 | S | C | 0.2254 | |
| 103 | G | C | 0.2163 | |
| 104 | S | C | 0.0000 | |
| 105 | F | C | 0.0000 | |
| 106 | A | C | 0.0660 | |
| 107 | Y | C | -0.1827 | |
| 108 | W | C | -0.8637 | |
| 109 | G | C | 0.0000 | |
| 110 | Q | C | -2.1008 | |
| 111 | G | C | -1.3882 | |
| 112 | T | C | -0.8133 | |
| 113 | L | C | -0.0770 | |
| 114 | V | C | 0.0000 | |
| 115 | T | C | -0.3970 | |
| 116 | V | C | 0.0000 | |
| 117 | S | C | -0.7317 | |
| 118 | A | C | -0.6431 | |
| 119 | A | C | -1.1400 | |
| 120 | K | C | -1.9120 | |
| 121 | T | C | -1.0721 | |
| 122 | T | C | -0.5940 | |
| 123 | P | C | -0.7900 | |
| 124 | P | C | 0.0000 | |
| 125 | S | C | -0.3528 | |
| 126 | V | C | 0.0000 | |
| 127 | Y | C | -0.5834 | |
| 128 | P | C | -0.5635 | |
| 129 | L | C | 0.0000 | |
| 130 | A | C | 0.0000 | |
| 131 | P | C | -0.0845 | |
| 132 | G | C | -0.7739 | |
| 133 | S | C | -0.9634 | |
| 134 | A | C | -0.6816 | |
| 135 | A | C | -0.7579 | |
| 136 | Q | C | -1.4994 | |
| 137 | T | C | -1.1070 | |
| 138 | N | C | -1.3464 | |
| 139 | S | C | -0.6536 | |
| 140 | M | C | 0.0795 | |
| 141 | V | C | -0.0925 | |
| 142 | T | C | 0.0956 | |
| 143 | L | C | 0.0000 | |
| 144 | G | C | 0.0000 | |
| 145 | C | C | 0.0000 | |
| 146 | L | C | 0.0000 | |
| 147 | V | C | 0.0000 | |
| 148 | K | C | -0.2137 | |
| 149 | G | C | -0.2712 | |
| 150 | Y | C | 0.0000 | |
| 151 | F | C | 0.0000 | |
| 152 | P | C | -1.0606 | |
| 153 | E | C | -1.1638 | |
| 154 | P | C | -0.9187 | |
| 155 | V | C | 0.0000 | |
| 156 | T | C | -0.3664 | |
| 157 | V | C | -0.1940 | |
| 158 | T | C | -0.3008 | |
| 159 | W | C | 0.0000 | |
| 160 | N | C | -1.0348 | |
| 161 | S | C | -0.7204 | |
| 162 | G | C | -0.5542 | |
| 163 | S | C | -0.4814 | |
| 164 | L | C | -0.2304 | |
| 165 | S | C | -0.3700 | |
| 166 | S | C | -0.3096 | |
| 167 | G | C | -0.2247 | |
| 168 | V | C | 0.1817 | |
| 169 | H | C | -0.1724 | |
| 170 | T | C | 0.0956 | |
| 171 | F | C | 0.0000 | |
| 172 | P | C | -0.1903 | |
| 173 | A | C | 0.2851 | |
| 174 | V | C | 0.8166 | |
| 175 | L | C | 1.1810 | |
| 176 | E | C | 0.0474 | |
| 177 | S | C | -0.6650 | |
| 178 | D | C | -1.4822 | |
| 179 | L | C | -0.5392 | |
| 180 | Y | C | 0.1265 | |
| 181 | T | C | 0.0000 | |
| 182 | L | C | 0.0000 | |
| 183 | S | C | 0.0000 | |
| 184 | S | C | 0.0000 | |
| 185 | S | C | 0.0000 | |
| 186 | V | C | 0.0000 | |
| 187 | T | C | 0.1069 | |
| 188 | V | C | 0.0000 | |
| 189 | P | C | -0.2152 | |
| 190 | S | C | -0.6084 | |
| 191 | S | C | -0.7256 | |
| 192 | T | C | -0.8615 | |
| 193 | W | C | 0.0000 | |
| 194 | P | C | -0.7297 | |
| 195 | S | C | -1.3109 | |
| 196 | E | C | -2.0981 | |
| 197 | T | C | -1.1914 | |
| 198 | V | C | 0.0000 | |
| 199 | T | C | 0.0000 | |
| 200 | C | C | 0.0000 | |
| 201 | N | C | 0.0000 | |
| 202 | V | C | 0.0000 | |
| 203 | A | C | -0.9547 | |
| 204 | H | C | 0.0000 | |
| 205 | P | C | -0.8289 | |
| 206 | A | C | -0.4702 | |
| 207 | S | C | -0.7028 | |
| 208 | S | C | -0.7456 | |
| 209 | T | C | -0.9897 | |
| 210 | K | C | -1.9622 | |
| 211 | V | C | -1.5554 | |
| 212 | D | C | -2.5040 | |
| 213 | K | C | -1.9331 | |
| 214 | K | C | -1.9354 | |
| 215 | I | C | 0.0000 | |
| 216 | V | C | 0.7332 | |
| 217 | P | C | -0.2511 | |
| 218 | R | C | -0.8863 | |
| 219 | D | C | -1.4013 | |
| 220 | C | C | -0.3481 |
Calculations for various pH values
This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.
pH |
Average A4D Score |
Max A4D Score |
|||
| 4.0 | -0.5907 | 2.7078 | View | CSV | PDB |
| 4.5 | -0.6397 | 2.6222 | View | CSV | PDB |
| 5.0 | -0.6966 | 2.5294 | View | CSV | PDB |
| 5.5 | -0.7521 | 2.436 | View | CSV | PDB |
| 6.0 | -0.7967 | 2.3465 | View | CSV | PDB |
| 6.5 | -0.823 | 2.2637 | View | CSV | PDB |
| 7.0 | -0.8309 | 2.1867 | View | CSV | PDB |
| 7.5 | -0.8259 | 2.1144 | View | CSV | PDB |
| 8.0 | -0.8127 | 2.0492 | View | CSV | PDB |
| 8.5 | -0.7913 | 1.9991 | View | CSV | PDB |
| 9.0 | -0.7595 | 1.974 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine